Biodiversity conservation policies are intrinsically related to ethnic issues in the Bolivian Amazon. The great social diversity that prevails in Bolivia is rooted in specific institutional arrangements according to categories which make the implementation of participatory mechanisms difficult to carry out. The present case study investigates the relation between social diversity and co-management governance of the Biosphere Reserve and Indigenous Territory of Pilón Lajas, located in the Beni department of Bolivia. Starting in the 1960s, productivist colonisation policies brought thousands of Quechua and Aymara people into the Amazonian areas, bringing with them their culti- vation methods as well as their social institutions. In the face of this wave of migration, populations considered indigenous, the Tsimane' and Mosetene, had to adapt by adopting some non-native practices. These new forms of collaboration seriously call into question the borders of the protected areas, making it difficult to apply the principles of nature conservation, especially in the buffer zone of the Biosphere Reserve but also in some parts of the core zone. The election of Evo Morales foretells a reconfiguration of the baselines between eastern and western Bolivia with regard to conservation policy.